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<h1>Mass detection</h1>

<h2>Description</h2>

<p>
The Mass detection module generates a list of masses (ions) for each scan in the raw data file.
Several algorithms are provided for this step.
The choice of the optimal algorithm depends on the raw data characteristics (mass resolution, mass precision, peak shape, noise).
In case the raw data is already centroided, only one algorithm (Centroid mass detector) can be used.
Other algorithms work only with continuous type data.
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<p>
When mass lists are generated for all MS level 1 scans, a green check mark will appear at the icon of the raw data file.
Each mass list can be opened by expanding individual scans from the project tree:<br>
<img src="masslist_open.png">
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<h4>Method parameters</h4>
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<dt>Mass detector</dt>
<dd>Algorithm to use for mass detection and its parameters</dd>

<dt>MS level</dt>
<dd>MS level of scans, for which the mass lists should be generated</dd> 

<dt>Mass list name</dt>
<dd>Name of the new mass list. If the processed scans already have a mass list of that name, it will be replaced.</dd>

<dt>CDF Filename (optional)</dt>
	<dd> If the box is checked, the user may specify a file in which the results of mass detection
	(centroiding) are saved. The file type will be CDF and the file will be formatted
	so that MZmine 2, or other software, will read it as a centroided data file. </dd>

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